1AM2 - JenaLib

Title :   GYRA INTEIN FROM MYCOBACTERIUM XENOPI

Authors :   T. Klabunde, S. Sharma, J. C. Sacchettini

Date :   20 Jun 97 (Deposition) - 24 Jun 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Intein, Protein Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Klabunde, S. Sharma, A. Telenti, W. R. Jacobs Jr. , J. C. Sacchettini
Crystal Structure Of Gyra Intein From Mycobacterium Xenopi Reveals Structural Basis Of Protein Splicing.
Nat. Struct. Biol. V. 5 31 1998
PubMed-ID: 9437427 | Reference-DOI: 10.1038/NSB0198-31
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTEIN_N_TER	PS50817	Intein N-terminal splicing motif profile.	GYRA_MYCXE	66-144	1	A:2-79
2	INTEIN_C_TER	PS50818	Intein C-terminal splicing motif profile.	GYRA_MYCXE	241-264	1	A:176-198

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTEIN_N_TER	PS50817	Intein N-terminal splicing motif profile.	GYRA_MYCXE	66-144	2	A:2-79
2	INTEIN_C_TER	PS50818	Intein C-terminal splicing motif profile.	GYRA_MYCXE	241-264	2	A:176-198

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:181
 aligned with GYRA_MYCXE | P72065 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:199
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         
           GYRA_MYCXE    65 YCITGDALVALPEGESVRIADIVPGARPNSDNAIDLKVLDRHGNPVLADRLFHSGEHPVYTVRTVEGLRVTGTANHPLLCLVDVAGVPTLLWKLIDEIKPGDYAVIQRSAFSVDCAGFARGKPEFAPTTYTVGVPGLVRFLEAHHRDPDAQAIADELTDGRFYYAKVASVTDAGVQPVYSLRVDTADHAFITNGFVSHN 263
               SCOP domains d1am2a_ A: GyrA intein                                                                                                                                                                                  SCOP domains
               CATH domains 1am2A00 A:0-198 Endonuclease - Pi-scei; Chain A, domain 1                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....eeehhh........eeee..eeee.....eeeeeeeee..eeeeeeee.....eeeee...eeeeeeee..eeeeeeeehhh.....eeeeehhh..------------------......hhhhhhh......hhhhhhhhh...eeeee..eeeeeeeee.eeeee.....eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -INTEIN_N_TER  PDB: A:2-79 UniProt: 66-144                                      ------------------------------------------------------------------------------------------------INTEIN_C_TER            PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1am2 A   0 ASITGDALVALPEGESVRIADIVPGARPNSDNAIDLKVLDRHGNPVLADRLFHSGEHPVYAVRTVEGLRVTGTANHPLLCLVDVAGVPTLLWKLIDEIKPGDYAVIQRSAFS------------------TVGVPGLVRFLEAHHRDPDAKAIADELTDGRFYYAKVASVTDAGVQPVYSLRVDTADHAFITNGFVSHN 198
                                     9        19        29        39        49        59        69        79        89        99       109 |       -         -|      139       149       159       169       179       189         
                                                                                                                                         111                130

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Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (GYRA_MYCXE | P72065)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003916	DNA topoisomerase activity	Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
	GO:0003918	DNA topoisomerase type II (ATP-hydrolyzing) activity	Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0006265	DNA topological change	The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
	GO:0016539	intein-mediated protein splicing	The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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